I'm not going to support the gross generalization that an entire country needs to be humbled, BUT: the shrine is a flashpoint of Japanese ultra-nationalism, which is on the rise.
Common ultra-nationalist beliefs are fairly odious: e.g. Japan should be applauded for liberating much of East Asia from Western colonial powers, the 1946-1948 Tokyo War Crimes tribunals were illegitimate, and the killings by Imperial Japanese troops during the 1937 "Nanjing massacre" were exaggerated or fabricated.
Those things are true, but the OP said that "Japan" has to be taken down.
As a not unrelated aside, nationalism is on the rise everywhere and if this doesn't change there will be new wars and possibly another (very) big one. I am personally freaked out very much by the rise of nationalism in the EU where I live. I'm not one to trivialise waving flags at a war memorial.
But- again, why does this indict the entire of Japan? Are all Japanese likely to go wave imperial flags at Meiji?
Common ultra-nationalist beliefs are fairly odious: e.g. Japan should be applauded for liberating much of East Asia from Western colonial powers, the 1946-1948 Tokyo War Crimes tribunals were illegitimate, and the killings by Imperial Japanese troops during the 1937 "Nanjing massacre" were exaggerated or fabricated.